北~中琉球に分布するアオカナヘビは、サキシマカナヘビと比べて背鱗の列数が少なく(10~14列 vs 10列以下)、鼠径孔の数も少ない(2~3対 vs 1対)。宮古諸島に分布するミヤコカナヘビはサキシマカナヘビと比べて腹板の列数が多い(6列 vs 8列)。サキシマカナヘビは上唇上に黒線が見られるものの、他2種では見られない[6, 7]
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